Décrypthon grid - grid resources dedicated to neuromuscular disorders.

Thanks to the availability of computational grids and their middleware, a seamless access to computation and storage resources is provided to application developers and scientists. The Décrypthon project is one example of such a high performance platform. In this paper, we present the architecture of the platform, the middleware developed to facilitate access to several servers deployed in France, and the data center for integrating large biological datasets over multiple sites, supported by a new query language and integration of various tools. The SM2PH project represents an example of a biological application that exploits the capacities of the Décrypthon grid. The goal of SM2PH is a better understanding of mutations involved in human monogenic diseases, their impact on the 3D structure of the protein and the subsequent consequences for the pathological phenotypes.

Confirmation of TFAP2A gene involvement in branchio-oculo-facial syndrome (BOFS) and report of temporal bone anomalies.

Branchio-oculo-facial syndrome (BOFS) is an autosomal-dominant condition characterized by three main features, respectively: branchial defects, ocular anomalies, and craniofacial defects including cleft lip and/or palate (CL/P). We report on one family with three affected, and two sporadic cases that have been found to carry missense mutations in the newly reported BOFS gene: TFAP2A. This report confirms the involvement of this transcription factor in this developmental syndrome with clinical variability. Moreover, we present CT scan temporal bone anomalies in the familial cases, related to branchial arch defects, highlighting the importance of radiological investigations for differential diagnosis.

MAGOS: multiple alignment and modelling server.

UNLABELLED: MAGOS is a web server allowing automated protein modelling coupled to the creation of a hierarchical and annotated multiple alignment of complete sequences. MAGOS is designed for an interactive approach of structural information within the framework of the evolutionary relevance of mined and predicted sequence information. AVAILABILITY: The web server is freely available at http://pig-pbil.ibcp.fr/magos.

The structure of Staphylococcus aureus epidermolytic toxin A, an atypic serine protease, at 1.7 A resolution.

BACKGROUND: Staphylococcal epidermolytic toxins A and B (ETA and ETB) are responsible for the staphylococcal scalded skin syndrome of newborn and young infants; this condition can appear just a few hours after birth. These toxins cause the disorganization and disruption of the region between the stratum spinosum and the stratum granulosum--two of the three cellular layers constituting the epidermis. The physiological substrate of ETA is not known and, consequently, its mode of action in vivo remains an unanswered question. Determination of the structure of ETA and its comparison with other serine proteases may reveal insights into ETA's catalytic mechanism. RESULTS: The crystal structure of staphylococcal ETA has been determined by multiple isomorphous replacement and refined at 1.7 A resolution with a crystallographic R factor of 0.184. The structure of ETA reveals it to be a new and unique member of the trypsin-like serine protease family. In contrast to other serine protease folds, ETA can be characterized by ETA-specific surface loops, a lack of cysteine bridges, an oxyanion hole which is not preformed, an S1 specific pocket designed for a negatively charged amino acid and an ETA-specific specific N-terminal helix which is shown to be crucial for substrate hydrolysis. CONCLUSIONS: Despite very low sequence homology between ETA and other trypsin-like serine proteases, the ETA crystal structure, together with biochemical data and site-directed mutagenesis studies, strongly confirms the classification of ETA in the Glu-endopeptidase family. Direct links can be made between the protease architecture of ETA and its biological activity.

Measurement of aortic blood flow by Doppler echocardiography: day to day variability in normal subjects and applicability in clinical research.

To assess the reliability of Doppler ultrasound for detecting serial changes in cardiac output in response to experimental interventions, the day to day variability of the minute distance of aortic flow was determined in seven normal subjects maintained in a tightly controlled environment with regard to diet and activities. Measurements were made at the same time on 5 to 6 sequential days from an apical window with use of both continuous wave and pulsed wave Doppler techniques. Two statistical measures of reliability were calculated, the intraclass coefficient of correlation (R), which varies between 0 (null reliability) and +1 (perfect reliability), and the 95% confidence interval for the error-free value of a single measurement. For sequential measurements of arterial pressure, 24 h urinary volume and sodium excretion and body weight, the intraclass coefficients of correlation ranged from 0.85 to 0.99, indicating low day to day variability consistent with tight environmental control. Continuous and pulsed wave modes were proved equally and highly reliable for measuring minute distance of aortic flow. However, continuous wave Doppler ultrasound provided acceptable signals more frequently than did the pulsed wave technique. For continuous wave Doppler ultrasound, R was 0.87 (p less than 0.00001); the 95% confidence interval was +/- 1.81 m/min (or 11% of the mean of all measurements), which indicates that this method can be used in a single individual to detect a greater than 11% change in minute distance measured once before and after an intervention.(ABSTRACT TRUNCATED AT 250 WORDS)

Long-term follow-up of patients after transcatheter direct current ablation of the atrioventricular junction.

The long-term follow-up study (41 +/- 23 months) of 47 patients undergoing direct current ablation because of drug-resistant supraventricular arrhythmias is reported. Significant early complications occurred in four patients and included hypotension, pericarditis, nonsustained polymorphic ventricular tachycardia and one sudden death. In 42 patients (86%), complete atrioventricular (AV) block was initially achieved. During the follow-up period, AV conduction resumed in 2 of these 42 patients. Of the seven patients in whom ablation was unsuccessful, two developed late complete AV block and three had symptomatic improvement. An improved activity level was reported among 83% of the patients with successful ablation. Health care utilization manifest as the number of hospital admissions per year before and after ablation decreased significantly after ablation (2.4 +/- 2.0 versus 0.3 +/- 0.5, p less than 0.001). Echocardiographic evaluation in five patients with a depressed left ventricular ejection fraction (27 +/- 7%) before ablation showed a significant increase (45 +/- 14%, p less than 0.05) after an average follow-up period of 31 months. New onset of congestive heart failure occurred after ablation in four patients, of whom two had no structural heart disease. The total mortality rate, including the one patient with sudden death, was 17% and was significantly higher among patients with underlying structural heart disease. Transcatheter direct current ablation is an effective treatment in patients with drug-resistant supraventricular tachycardia, providing a beneficial long-term outcome including an improved quality of life and a decrease in health care utilization.(ABSTRACT TRUNCATED AT 250 WORDS)

Bone mineral decrease in the leg with unilateral chronic occlusive arterial disease.

OBJECTIVE: The links between osteoporosis and arteriosclerosis have been established by numerous epidemiological studies. Could arteriosclerosis induce bone mineral loss via ischemia or other pathological process? We carried out a comparative study of bone mineral density in both legs of patients with unilateral arterial disease of the lower limbs. METHODS: We studied 25 patients, 22 men and 3 women, whose mean age was 62.3 years (range 35-88 years). These patients had unilateral lower limb arterial disease of at least 3 months duration with a systolic index at least 50% lower on the affected than on the healthy side. Bone mineral content (BMC) and bone mineral densities (BMD) of the femoral neck, femur, tibia, foot and ankle of the affected and the unaffected legs were measured by dual x-ray absorptiometry (Lunar DPXL) and the results compared. RESULTS: Bone mineral density was significantly lower in the femur (-3.7%, p = 0.04), the foot and the ankle (-3%, p = 0.05) of the affected leg. There was a non-significant decrease in BMD of the whole femoral neck (-1.2%) and the trochanter (-4.4%, p = 0.08) on the affected side. Tibial bone mineral density was identical in both legs. Bone mineral content was lower on the affected side (-5.3%, p = 0.05) whereas fat mass and muscle mass were the same in both legs. CONCLUSION: The ischemia resulting from arterial disease of the lower limbs appears to have a direct deleterious effect on bone mineralization.

Stenosis of the lumbar spinal canal in vertebral ankylosing hyperostosis.

Certain morphologic features frequently observed in radiography or computed tomography (CT) scan in patients with hyperostosis led us to study the association between a narrowed spinal canal and vertebral hyperostosis. Twenty-eight items were selected and studied by three different investigators (two rheumatologists and one radiologist) in radiographs and CT scans of 100 patients with acquired stenosis of the lumbar canal, with or without hyperostosis (46 and 54 cases, respectively). The most distinctive points that we suggest can be used as diagnostic criteria of the hyperostotic narrowed lumbar canal are anterior or posterior lateral marginal somatic osseous proliferations, proliferations of the nonarticular aspects of the posterior apophyses, and ossifications of the posterior articular capsule and of the ligaments (yellow ligament, posterior longitudinal ligament, and the supraspinal ligament). Four of these six criteria should be present to establish the diagnosis of hyperostotic lumbar stenosis. The appearance of lumbar hyperostosis on X-ray or CT scans differs from that of simple degenerative changes due to arthrosis, and the hyperostosis can be held responsible for dural compression.

Breast granuloma and C.R.S.T. syndrome.

One case of CRST syndrome with breast granuloma is presented. The presumed diagnosis were infectious or neoplastic diseases. High doses of corticosteroids led to improvement in breast nodules.

Lumbar and cervical stenosis. Frequency of the association, role of the ankylosing hyperostosis.

The authors report a study of 47 patients admitted for cervical myelopathy (N = 17) or symptomatic lumbar spinal stenosis (N = 30). Nine patients had clinical evidence of coexisting cervical myelopathy and lumbar spinal stenosis. Ten out of the 17 patients having cervical myelopathy had lumbar spinal stenosis as evidenced by sagittal tomography and/or computerized tomography. Nine out of the 30 patients admitted for symptomatic lumbar spinal stenosis had coexisting cervical canal stenosis as evidenced by sagittal tomography. Thirteen out of these 19 patients with both cervical and lumbar canal stenosis had also ankylosing spinal hyperostosis.

Inflammatory rheumatism and nasal polyposis.

We report five cases of seronegative inflammatory rheumatism associated with nasal polyposis. The patients were four women and one man, mean age 49.5 years (range 42-59 yrs.). Two patients had polyarthralgia predominating in the hands, wrists and knees and two patients had symmetrical acromelic polyarthritis. The fifth patient, a woman, had oligoarticular arthritis. In a single female patient, X-rays showed moderate erosions of both tarsometatarsal bones. The inflammatory syndrome was moderate with mean ESR 23 (12-38) and immunological investigations were negative except for the presence of pANCA (50-200 U) in three patients. HLA-A1, B8, and Bw35 antigens were found in three of the five patients. In all cases, nasal and sinus polyposis (NSP) preceded rheumatism and the joint symptoms were accompanied by worsening of the ENT symptoms. NSP was confirmed by CT scan of the nasal fossae and sinuses. Polyps were surgically removed in four patients and the histology showed neither granuloma nor vasculitis. In four patients the joint symptoms, which responded poorly to nonsteroidal anti-inflammatory drugs (NSAIDs), improved markedly after ENT treatment (surgery and topical steroids) and synthetic antimalarials. The concomitant course of the joint and ENT symptoms suggests there may be a link between inflammatory rheumatism and NSP.

[Cerebral ischemic accidents and chronic disseminated intravascular coagulation of cancerous origin]. / Accidents ischemiques cérébraux et coagulation intravasculaire disséminée chronique d'origine cancéreuse.

Cerebral infarcts in 3 patients revealed the presence of disseminated intravascular coagulation (DIVC) of cancerous origin before any clinical manifestations of the neoplasm. Neurologic manifestations of these consumption coagulopathies almost constantly produce a picture of diffuse encephalopathy, expression of disseminated microinfarcts; however, transient or constituted focalized ischemic accidents by occlusion of a medium sized artery are also possible, and this in the absence of non-bacterial thrombotic endocarditis. Biologic diagnosis of DIVC is not always simple, and screening tests (platelet count, prothrombin and fibrinogen levels) can remain within normal limits during chronic forms, as a result of a subjacent inflammatory syndrome, frequently associated with cancer. Two other specific serum tests are therefore of fundamental interest: assay of fibrin degradation products and tests for soluble complexes.

[Osteocalcin and smoking]. / Ostéocalcine et tabagisme.

Smoking is a risk factor for osteoporosis. Nicotine and nonnicotine tobacco smoke components have been shown to depress osteoblast activity in a number of in vitro and animal studies. To determine whether smoking is associated with depressed osteoblast activity in humans, we measured serum osteocalcin levels (using a radioimmunological method based on an antibody to human osteocalcin) in 24 male or female smokers and 24 matched nonsmokers. Overall, osteocalcin levels were significantly lower in smokers (15 +/- 6.95 ng/ml) than in nonsmokers (21.27 +/- 8.34 ng/ml) (p = 0.007). The difference between smokers and nonsmokers was significant in males (15.3 +/- 4.5 vs 23.27 +/- 9.7; p = 0.02) but not in females (16.27 +/- 8.9 vs 19.45 +/- 6.7; p = 0.2). These data suggest that smoking may induce osteoblast depression, either directly or via hormonal changes.

[Rheumatic manifestations of chronic hepatitis C and response to the treatment with interferon alpha-2b]. / Manifestations rhumatologiques des hépatites C chroniques et réponse au traitement par interféron alpha-2b.

Chronic hepatitis C can be responsible for a broad range of autoimmune manifestations, including cryoglobulinemia and Sjögren's syndrome. We report our experience with six patients (five women and one man; mean age 55.6 years) in whom hepatitis C was diagnosed during evaluation of joint symptoms. Polyarthralgia was the main symptom and was often accompanied with myalgia; a polyalgic syndrome was seen in some patients. Isolated cytolysis was consistently found, although, in some instances, liver enzyme elevations were moderate and postdated the onset of the clinical symptoms. The diagnosis of hepatitis C was confirmed by recombinant immunoblot assay (RIBA) in every case. The polymerase chain reaction (PCR) detected hepatitis C virus RNA in five of the six patients. Histological findings were characteristic of chronic hepatitis. All six patients had immunological test abnormalities, which included presence of rheumatoid factors (2 of 6), positive antinuclear antibodies without anti-DNA antibodies (3 of 6) and low serum complement levels (3 of 6). A cryoprecipitate was found in four of the six patients. Four patients reported symptoms of sicca syndrome and two had Chisholm grade III lesions upon examination of salivary gland biopsy specimens. Four patients were given a six-month course of interferon alpha. In three of these four patients, evaluation at the end of the treatment showed abatement or resolution of symptoms, normal liver function tests, unchanged or diminished antinuclear antibody titers, and normal serum complement levels. In the remaining patient, no changes in symptoms or transaminase levels occurred during interferon alpha treatment. In conclusion, rheumatic symptoms can be the most prominent manifestation of chronic hepatitis C.(ABSTRACT TRUNCATED AT 250 WORDS)

[Increase of CA 19.9 in dysimmune inflammatory rheumatism. Apropos of 6 cases]. / Elévation du CA 19.9 au cours des rhumatismes inflammatories dysimmunitaires. A propos de 6 observations.

CA 19.9 is a marker for several cancers, including ductal adenocarcinomas of the pancreas. CA 19.9 elevation is rarely found in patients without benign or malignant digestive system disease. We studied serum CA 19.9 levels in patients with a variety of inflammatory joint diseases, including rheumatoid arthritis (n = 20), lupus, Sjögren's syndrome or U1RNP-associated connective tissue syndrome (Sharp's syndrome) (n = 11), dermatopolymyositis (n = 8), and giant cell arteritis or polymyalgia rheumatica (n = 8). The mean CA 19.9 level in each of these groups was not significantly different from the value seen in a group of patients with osteoporosis. Six patients had persistent marked elevation in serum CA 19.9 levels. Two had Sjögren's syndrome, two had Sharp's syndrome and two had dermatopolymyositis. None of these six patients had evidence of tumoral disease despite a follow-up of several years. Likely explanations for the CA 19.9 elevation were chronic pancreatitis in one case and lung disease in the other five. In patients with lung involvement due to inflammatory joint disease, CA 19.9 elevation may indicate severe disease and may be of use for monitoring the lung condition.

SPINE bioinformatics and data-management aspects of high-throughput structural biology.

SPINE (Structural Proteomics In Europe) was established in 2002 as an integrated research project to develop new methods and technologies for high-throughput structural biology. Development areas were broken down into workpackages and this article gives an overview of ongoing activity in the bioinformatics workpackage. Developments cover target selection, target registration, wet and dry laboratory data management and structure annotation as they pertain to high-throughput studies. Some individual projects and developments are discussed in detail, while those that are covered elsewhere in this issue are treated more briefly. In particular, this overview focuses on the infrastructure of the software that allows the experimentalist to move projects through different areas that are crucial to high-throughput studies, leading to the collation of large data sets which are managed and eventually archived and/or deposited.

A domain in the N-terminal extension of class IIb eukaryotic aminoacyl-tRNA synthetases is important for tRNA binding.

Cytoplasmic aspartyl-tRNA synthetase (AspRS) from Saccharomyces cerevisiae is a homodimer of 64 kDa subunits. Previous studies have emphasized the high sensitivity of the N-terminal region to proteolytic cleavage, leading to truncated species that have lost the first 20-70 residues but that retain enzymatic activity and dimeric structure. In this work, we demonstrate that the N-terminal extension in yeast AspRS participates in tRNA binding and we generalize this finding to eukaryotic class IIb aminoacyl-tRNA synthetases. By gel retardation studies and footprinting experiments on yeast tRNA(Asp), we show that the extension, connected to the anticodon-binding module of the synthetase, contacts tRNA on the minor groove side of its anticodon stem. Sequence comparison of eukaryotic class IIb synthetases identifies a lysine-rich 11 residue sequence ((29)LSKKALKKLQK(39) in yeast AspRS with the consensus xSKxxLKKxxK in class IIb synthetases) that is important for this binding. Direct proof of the role of this sequence comes from a mutagenesis analysis and from binding studies using the isolated peptide.